Biomedical subjects

M Baiesi

Publications and source records attributed to M Baiesi.

5 recordsLinked to original sources

PubMed2003

RNA denaturation: excluded volume, pseudoknots, and transition scenarios.

A lattice model of RNA denaturation which fully accounts for the excluded volume effects among nucleotides is proposed. A numerical study shows that interactions forming pseudoknots must be included in order to get a sharp continuous transition. Otherwise a smooth crossover occurs from the swollen linear polymer behavior to highly ramified, almost compact conformations with secondary structures. In the latter scenario, which is appropriate when these structures are much more stable than pseudoknot links, probability distributions for the lengths of both loops and main branches obey scaling with nonclassical exponents.

Models, Chemical↗

PubMed2003

Scale-free networks from a Hamiltonian dynamics.

Contrary to many recent models of growing networks, we present a model with fixed number of nodes and links, where a dynamics favoring the formation of links between nodes with degree of connectivity as different as possible is introduced. By applying a local rewiring move, the network reaches equilibrium states assuming broad degree distributions, which have a power-law form in an intermediate range of the parameters used. Interestingly, in the same range we find nontrivial hierarchical clustering.

Journal Article↗

PubMed2003

Interstrand distance distribution of DNA near melting.

The distance distribution between complementary base pairs of the two strands of a DNA molecule is studied near the melting transition. Scaling arguments are presented for a generalized Poland-Scheraga-type model that includes self-avoiding interactions. At the transition temperature and for a large distance r, the distribution decays as 1/r(kappa) with kappa=1+(c-2)/nu. Here nu is the self-avoiding walk correlation length exponent and c is the exponent associated with the entropy of an open loop in the chain. Results for the distribution function just below the melting point are also presented. Numerical simulations that fully take into account the self-avoiding interactions are in good agreement with the scaling approach.

Journal Article↗

PubMed2001

Peculiar scaling of self-avoiding walk contacts.

The nearest neighbor contacts between the two halves of an N-site lattice self-avoiding walk offer an unusual example of scaling random geometry: for N-->infinity they are strictly finite in number but their radius of gyration R(c) is power law distributed proportional to R(-tau)(c), where tau>1 is a novel exponent characterizing universal behavior. A continuum of diverging length scales is associated with the R(c) distribution. A possibly superuniversal tau = 2 is also expected for the contacts of a self-avoiding or random walk with a confining wall.

Journal Article↗

PubMed2001

Zipping and collapse of diblock copolymers.

Using exact enumeration methods and Monte Carlo simulations, we study the phase diagram relative to the conformational transitions of a diblock copolymer in two dimensions. The polymer is made of two homogeneous strands of monomers of different species which are joined to each other at one end. We find that, depending on the values of the energy parameters in the model, there is either a first order collapse from a swollen phase to a compact phase of spiral type, or a continuous transition to an intermediate zipped phase followed by a first order collapse at lower temperatures. Critical exponents of the zipping transition are computed, and their exact values are conjectured on the basis of a mapping onto percolation geometry, thanks to recent results on path-crossing probabilities.

Journal Article↗